Sodium in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb 2pcg)

The binding sites of Sodium atom in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2pcg). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2pcg structure was solved by M.SUGAHARA, M.TAKETA, Y.KAGEYAMA, Y.MATSUURA, N.KUNISHIMA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.9-2.2 Space group P41212 a (A) 104.926 b (A) 104.926 c (A) 138.916 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 23 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2pcg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2pcg. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr117, A: Ile127, A: Phe130, A: Gly131, B: Tyr117, B: Phe130, B: Gly131, B: Ser133, A: Hoh610, A: Hoh752, B: Hoh270, B: Hoh271, B: Hoh273, B: Hoh276, B: Hoh279, B: Hoh284, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.82 Na CZ A:Tyr117 3.43 Na CE1 A:Tyr117 4.42 Na OH A:Tyr117 2.61 Na O A:Ile127 4.24 Na O A:Phe130 4.22 Na CB A:Phe130 4.17 Na C A:Phe130 4.76 Na CA A:Phe130 4.99 Na O A:Gly131 4.95 Na CD1 B:Tyr117 4.20 Na CE1 B:Tyr117 4.09 Na CB B:Phe130 4.59 Na O B:Gly131 3.98 Na OG B:Ser133 4.12 Na O A:Hoh610 4.30 Na O A:Hoh752 2.11 Na O B:Hoh270 2.21 Na O B:Hoh271 2.62 Na O B:Hoh273 4.50 Na O B:Hoh276 2.51 Na O B:Hoh279 4.62 Na O B:Hoh284 4.97 interactive model: